Follow Python standard packaging guidelines

[jan-janssen]

Summary by CodeRabbit

• Chores
  • Updated CI/CD workflows to reflect the project's source layout and ensure build/format steps target the correct paths.
  • Adjusted packaging and tooling configuration so versioning, distribution, and coverage now reference the updated source structure.

[coderabbitai]

Walkthrough

The repository is moved to a src-layout: CI workflows and build tooling references updated to use src/pylammpsmpi/ (including the _version.py location and Black source paths); build steps otherwise remain unchanged.

Changes

Cohort / File(s)	Summary
CI workflow updates .github/workflows/deploy.yml, .github/workflows/pipeline.yml	Updated paths used in CI: git update-index now marks src/pylammpsmpi/_version.py unchanged (instead of pylammpsmpi/_version.py), and Black workflow/source path references changed from ./${{ github.event.repository.name }} to ./src/${{ github.event.repository.name }}.
Build & packaging config pyproject.toml	Updated packaging and tooling references (version-file, sdist/wheel entries, version source path, coverage settings) to point to src/pylammpsmpi/ instead of pylammpsmpi/.

Sequence Diagram(s)

No sequence diagram included — changes are limited to path/config updates with no new runtime control flow.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Switch from versioneer to hatchling #360: Related hatchling/version-file changes that touch the same version-file and src-layout path locations.

Poem

🐰
Hopping through src with organized glee,
Paths relaid neatly for all to see,
CI and build now point where they should,
A tidy repo — tidy and good! 🥕✨

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title Check	✅ Passed	The title "Follow Python standard packaging guidelines" is directly related to the main changes in the pull request. The pull request systematically restructures the project to adopt the src-layout pattern by updating references from pylammpsmpi/ to src/pylammpsmpi/ across deployment workflows, pipeline workflows, and project configuration files. The src-layout is a recognized Python standard packaging guideline recommended by the Python Packaging Authority. The title accurately conveys the primary intent of implementing this packaging convention, and a teammate scanning the git history would clearly understand the purpose of this changeset.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch refactor

---

📜 Recent review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between ef2a017 and d720293.

📒 Files selected for processing (1)

• pyproject.toml (2 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• pyproject.toml

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (1)

• GitHub Check: unittest_mpich_mac

---

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.41%. Comparing base (37df11b) to head (d720293).
⚠️ Report is 5 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #389      +/-   ##
==========================================
+ Coverage   85.17%   85.41%   +0.23%     
==========================================
  Files           6        7       +1     
  Lines         796      809      +13     
==========================================
+ Hits          678      691      +13     
  Misses        118      118              

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[coderabbitai]

Actionable comments posted: 1

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

pyproject.toml (1)

44-47: Update [tool.hatch.build] include for consistency with src-layout and best practices.

Global build configuration in the tool.hatch.build table is not recommended when target-specific config is present, as keys may then be overridden by target config. The global include = ["pylammpsmpi"] (line 46) refers to the root directory structure, while the build targets specify packages = ["src/pylammpsmpi"] (lines 93, 98). When packages is defined for a target, it relies on sources and takes precedence.

While hatch will correctly build using the target-specific packages, align the global include with the src-layout for consistency and clarity:

 [tool.hatch.build]
 include = [
-    "pylammpsmpi"
+    "src/pylammpsmpi"
 ]

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 9ec6334 and ef2a017.

📒 Files selected for processing (3)

• .github/workflows/deploy.yml (1 hunks)
• .github/workflows/pipeline.yml (2 hunks)
• pyproject.toml (2 hunks)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (3)

• GitHub Check: codecov/patch
• GitHub Check: unittest_openmpi_mac
• GitHub Check: unittest_mpich_mac

🔇 Additional comments (2)

.github/workflows/deploy.yml (1)

35-35: Version file path correctly updated for src-layout.

The git update-index command now correctly references the version file at its new location src/pylammpsmpi/_version.py, consistent with pyproject.toml configuration.

.github/workflows/pipeline.yml (1)

16-16: Black formatter paths correctly updated for src-layout.

Both the check job and auto-fix job now reference the source directory at its new location under src/. The paths are consistent and will correctly format the migrated package structure.

Also applies to: 32-32

[coderabbitai]

⚠️ Potential issue | 🔴 Critical

Coverage source path not updated to src-layout.

Line 106 still references the old package location ["pylammpsmpi"] instead of ["src/pylammpsmpi"]. This will cause coverage collection to fail after migration to the src-layout structure, as it won't find source files in their new location.

Apply this fix:

 [tool.coverage.run]
-source = ["pylammpsmpi"]
+source = ["src/pylammpsmpi"]
 command_line = "-m unittest discover tests"

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change

	source = ["pylammpsmpi"]
	[tool.coverage.run]
	source = ["src/pylammpsmpi"]
	command_line = "-m unittest discover tests"

🤖 Prompt for AI Agents

In pyproject.toml around line 106, the coverage source path still points to the
old package root ["pylammpsmpi"] but the repository uses src-layout; update the
path to ["src/pylammpsmpi"] so coverage tools can find sources under the src/
directory and regenerate/verify coverage by running the coverage collection/test
command after the change.